There is a huge inconsistency I just found out while playing morrowind, the kind that is completely immersion-breaking to me. I had become patriarch of the tribunal temple before the main quest reveals you that ALMSIVI are not what they pretend to be. My position was respected when I wandered in the ministery of truth, seeking Milo... but the game acts if I was just nothing among the temple as soon as some started to call me Nerevarine : I recieved a letter from someone that works for the former patriarch Saryoni, it explains that the temple (of which I am the partiarch) has decided that I was an outlaw and that his majesty the patriarch Saryoni would not even listen to me if I havn't the support of all Vvardenfell (Hortator + Nerevarine) before. But this Saryoni is my predecessor and has lost his function by now... and all these guys work for me... either I am excummuniated or Saryoni tells me that he wants to discuss the siutation or I recieve a letter directly from Vivec and jump the "convicing the temple" stage... I don't know but this was incoherent, the question was just not adressed in the original game.
You've understood the problem, and I think it is the kind of detail that changes everything if fixed. I have no solid idea about how to fix it in Skywind, that's why I think it should be discussed !
I didn't find a topic that was dealing with that question, sorry if it is just me who didn't see and hoping you can understand my english x)